First, it looks like you still have a lot of lead to be removed before you continue. Second, the area you're concerned with got leaded over on the forward face and the dash covered the lower surface once its installed. The solution would be to put seam sealer in the groove after the windshield is installed to keep moisture out of that area.
How is the fit of the cowl on the firewall lip - particularly wher it runs across and then turns up. I'm in the process now and it doesn't fit well there at all - big gaps !!